24FD

Technical details

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library(GeoPressureR)
library(leaflet)
library(leaflet.extras)
library(raster)
library(dplyr)
library(ggplot2)
library(kableExtra)
library(plotly)
library(GeoLocTools)
setupGeolocation()
knitr::opts_chunk$set(echo = FALSE)
load(paste0("../data/1_pressure/", params$gdl_id, "_pressure_prob.Rdata"))
load(paste0("../data/2_light/", params$gdl_id, "_light_prob.Rdata"))
load(paste0("../data/3_static/", params$gdl_id, "_static_prob.Rdata"))
load(paste0("../data/4_basic_graph/", params$gdl_id, "_basic_graph.Rdata"))

Settings used

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kable(gpr)

include	gdl_id	crop_start	crop_end	thr_dur	extent_N	extent_W	extent_S	extent_E	map_scale	map_max_sample	map_margin	prob_map_s	prob_map_thr	shift_k	calib_lon	calib_lat	calib_1_start	calib_1_end	calib_2_start	calib_2_end	calib_2_lon	calib_2_lat	prob_light_w	thr_prob_percentile	thr_gs	RingNo	scientific_name	common_name	mass	wing_span	Color
TRUE	24FD	1900-01-01	2100-01-01	16	50	20	-35	120	2	300	30	1	0.9	21600	110.69	48.59	2019-06-18 05:15:00	2019-08-10 12:35:00	NA	NA	NA	NA	0.1	0.9	120	NA	NA	Eurasian Nightjar	NA	NA	NA

Pressure timeserie

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pressure_na <- pam$pressure %>%
  mutate(obs = ifelse(isoutliar | sta_id == 0, NA, obs))
p <- ggplot() +
  geom_line(data = pam$pressure, aes(x = date, y = obs), colour = "grey") +
  geom_point(data = subset(pam$pressure, isoutliar), aes(x = date, y = obs), colour = "black") +
  # geom_line(data = pressure_na, aes(x = date, y = obs, color = factor(sta_id)), size = 0.5) +
  geom_line(data = do.call("rbind", shortest_path_timeserie) %>% filter(sta_id>0), aes(x = date, y = pressure0, col = factor(sta_id))) +
  theme_bw() +
  scale_colour_manual(values = col) +
  scale_y_continuous(name = "Pressure(hPa)")

ggplotly(p, dynamicTicks = T) %>% layout(showlegend = F)

Light

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raw_geolight <- pam$light %>%
  transmute(
    Date = date,
    Light = obs
  )
lightImage(tagdata = raw_geolight, offset = 0)
tsimagePoints(twl$twilight,
  offset = 0, pch = 16, cex = 1.2,
  col = ifelse(twl$deleted, "grey20", ifelse(twl$rise, "firebrick", "cornflowerblue"))
)
abline(v = gpr$calib_2_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_start, lty = 1, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_2_end, lty = 2, col = "firebrick", lwd = 1.5)
abline(v = gpr$calib_1_end, lty = 2, col = "firebrick", lwd = 1.5)

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hist(z, freq = F)
lines(fit_z, col = "red")

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li_s <- list()
l <- leaflet(width = "100%") %>%
  addProviderTiles(providers$Stamen.TerrainBackground) %>%
  addFullscreenControl()
for (i_r in seq_len(length(light_prob))) {
  i_s <- metadata(light_prob[[i_r]])$sta_id
  info <- pam$sta[pam$sta$sta_id == i_s, ]
  info_str <- paste0(i_s, " | ", info$start, "->", info$end)
  li_s <- append(li_s, info_str)
  l <- l %>% addRasterImage(light_prob[[i_r]], opacity = 0.8, colors = "OrRd", group = info_str)
}
l %>%
  addCircles(lng = gpr$calib_lon, lat = gpr$calib_lat, color = "black", opacity = 1) %>%
  addLayersControl(
    overlayGroups = li_s,
    options = layersControlOptions(collapsed = FALSE)
  ) %>%
  hideGroup(tail(li_s, length(li_s) - 1))

GeoPressureViz

To visualize the path on GeoPressureViz, you will need to also load the pressure and light probability map and align them first with the code below.

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sta_marginal <- unlist(lapply(static_prob_marginal, function(x) raster::metadata(x)$sta_id))
sta_pres <- unlist(lapply(pressure_prob, function(x) raster::metadata(x)$sta_id))
sta_light <- unlist(lapply(light_prob, function(x) raster::metadata(x)$sta_id))
pressure_prob <- pressure_prob[sta_pres %in% sta_marginal]
light_prob <- light_prob[sta_light %in% sta_marginal]

The code below will open with the shortest path computed with the graph approach. You can change it to

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geopressureviz <- list(
  pam_data = pam,
  static_prob = static_prob,
  static_prob_marginal = static_prob_marginal,
  pressure_prob = pressure_prob,
  light_prob = light_prob,
  pressure_timeserie = shortest_path_timeserie
)
save(geopressureviz, file = "~/geopressureviz.RData")

shiny::runApp(system.file("geopressureviz", package = "GeoPressureR"),
  launch.browser = getOption("browser")
)

Stationay period information

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pam$sta %>% kable()

start	end	sta_id
2019-06-15 00:00:00	2019-06-18 04:40:00	1
2019-06-18 05:15:00	2019-08-10 12:35:00	2
2019-08-10 13:10:00	2019-08-11 12:40:00	3
2019-08-11 13:15:00	2019-08-13 13:55:00	4
2019-08-13 16:25:00	2019-08-14 12:15:00	5
2019-08-14 19:35:00	2019-08-15 15:10:00	6
2019-08-15 20:20:00	2019-08-16 21:15:00	7
2019-08-16 21:20:00	2019-08-17 12:30:00	8
2019-08-17 12:45:00	2019-08-18 12:20:00	9
2019-08-18 13:00:00	2019-08-19 12:30:00	10
2019-08-19 12:30:00	2019-08-20 12:25:00	11
2019-08-20 12:55:00	2019-08-21 13:05:00	12
2019-08-21 13:10:00	2019-08-22 21:20:00	13
2019-08-22 21:35:00	2019-08-26 12:20:00	14
2019-08-26 21:50:00	2019-08-27 12:50:00	15
2019-08-27 21:55:00	2019-08-28 14:10:00	16
2019-08-28 17:30:00	2019-08-29 14:45:00	17
2019-08-29 20:50:00	2019-08-30 13:55:00	18
2019-08-30 22:20:00	2019-08-31 14:20:00	19
2019-08-31 17:00:00	2019-08-31 19:35:00	20
2019-08-31 22:25:00	2019-09-01 13:55:00	21
2019-09-01 22:50:00	2019-09-02 13:45:00	22
2019-09-02 22:00:00	2019-09-03 15:00:00	23
2019-09-03 23:00:00	2019-09-04 16:25:00	24
2019-09-04 16:40:00	2019-09-05 14:00:00	25
2019-09-05 14:35:00	2019-09-06 23:50:00	26
2019-09-07 00:15:00	2019-09-08 13:45:00	27
2019-09-08 14:10:00	2019-09-09 23:30:00	28
2019-09-10 00:10:00	2019-09-10 13:55:00	29
2019-09-10 15:15:00	2019-09-11 20:45:00	30
2019-09-11 20:50:00	2019-09-12 14:20:00	31
2019-09-12 14:40:00	2019-09-13 00:10:00	32
2019-09-13 00:10:00	2019-09-13 14:05:00	33
2019-09-13 14:15:00	2019-09-14 21:25:00	34
2019-09-14 21:30:00	2019-09-15 13:45:00	35
2019-09-15 14:00:00	2019-09-16 13:50:00	36
2019-09-16 14:05:00	2019-09-20 14:40:00	37
2019-09-20 18:20:00	2019-09-21 14:10:00	38
2019-09-21 19:00:00	2019-09-22 15:05:00	39
2019-09-22 17:10:00	2019-09-22 20:45:00	40
2019-09-23 00:50:00	2019-09-23 14:45:00	41
2019-09-24 00:00:00	2019-09-24 14:40:00	42
2019-09-24 17:00:00	2019-09-24 21:00:00	43
2019-09-25 00:50:00	2019-09-25 17:35:00	44
2019-09-26 00:25:00	2019-09-26 14:50:00	45
2019-09-27 01:35:00	2019-09-27 17:00:00	46
2019-09-27 20:20:00	2019-09-28 14:35:00	47
2019-09-28 23:30:00	2019-09-29 14:55:00	48
2019-09-30 01:50:00	2019-09-30 14:45:00	49
2019-10-01 02:00:00	2019-10-01 16:10:00	50
2019-10-01 23:45:00	2019-10-02 14:55:00	51
2019-10-02 19:50:00	2019-10-05 01:35:00	52
2019-10-05 01:35:00	2019-10-16 14:50:00	53
2019-10-16 16:10:00	2019-10-17 14:55:00	54
2019-10-18 01:50:00	2019-10-18 14:55:00	55
2019-10-18 15:05:00	2019-10-19 16:30:00	56
2019-10-19 20:30:00	2019-10-20 01:55:00	57
2019-10-20 02:20:00	2019-10-20 17:00:00	58
2019-10-20 21:40:00	2019-10-21 18:35:00	59
2019-10-21 19:40:00	2019-10-23 14:50:00	60
2019-10-23 15:20:00	2019-10-31 16:10:00	61
2019-10-31 18:15:00	2019-11-01 02:15:00	62
2019-11-01 02:30:00	2019-11-01 15:05:00	63
2019-11-01 15:35:00	2019-11-02 15:05:00	64
2019-11-02 15:35:00	2019-11-03 16:05:00	65
2019-11-03 16:55:00	2019-11-05 22:40:00	66
2019-11-06 02:25:00	2019-11-06 15:00:00	67
2019-11-07 02:10:00	2019-11-07 15:25:00	68
2019-11-08 01:10:00	2019-11-08 15:30:00	69
2019-11-09 00:15:00	2019-11-09 22:40:00	70
2019-11-10 00:10:00	2019-11-10 15:30:00	71
2019-11-10 16:25:00	2019-11-10 22:25:00	72
2019-11-11 00:55:00	2019-11-11 16:40:00	73
2019-11-11 18:05:00	2019-11-12 23:25:00	74
2019-11-13 00:15:00	2019-11-13 20:40:00	75
2019-11-13 21:30:00	2019-11-14 19:00:00	76
2019-11-15 02:10:00	2019-11-15 16:10:00	77
2019-11-16 02:25:00	2019-11-16 16:30:00	78
2019-11-17 00:15:00	2019-11-17 17:00:00	79
2019-11-18 02:05:00	2019-11-18 20:40:00	80
2019-11-19 00:15:00	2019-11-19 17:05:00	81
2019-11-19 19:20:00	2019-11-21 02:25:00	82
2019-11-21 02:35:00	2019-11-21 17:20:00	83
2019-11-22 01:30:00	2019-11-22 18:00:00	84
2019-11-23 02:30:00	2019-11-23 17:15:00	85
2019-11-23 21:20:00	2019-11-24 18:45:00	86
2019-11-25 02:15:00	2019-11-25 19:25:00	87
2019-11-25 20:20:00	2019-11-26 00:15:00	88
2019-11-26 01:15:00	2020-03-23 19:15:00	89
2020-03-24 03:25:00	2020-03-24 20:05:00	90
2020-03-25 03:25:00	2020-03-25 16:25:00	91
2020-03-25 20:20:00	2020-03-26 16:10:00	92
2020-03-26 21:25:00	2020-03-27 16:00:00	93
2020-03-27 17:25:00	2020-03-27 21:20:00	94
2020-03-28 03:15:00	2020-03-28 16:25:00	95
2020-03-29 03:10:00	2020-03-29 16:30:00	96
2020-03-30 02:55:00	2020-03-30 16:15:00	97
2020-03-31 02:45:00	2020-03-31 15:45:00	98
2020-04-01 03:00:00	2020-04-01 16:25:00	99
2020-04-02 01:50:00	2020-04-02 22:20:00	100
2020-04-03 02:50:00	2020-04-03 15:30:00	101
2020-04-04 02:50:00	2020-04-04 18:10:00	102
2020-04-04 19:00:00	2020-04-04 19:10:00	103
2020-04-04 21:00:00	2020-04-05 02:25:00	104
2020-04-05 02:40:00	2020-04-05 15:20:00	105
2020-04-05 16:20:00	2020-04-05 21:55:00	106
2020-04-05 22:35:00	2020-04-06 15:30:00	107
2020-04-06 16:15:00	2020-04-06 23:05:00	108
2020-04-06 23:45:00	2020-04-07 15:50:00	109
2020-04-07 17:55:00	2020-04-08 16:10:00	110
2020-04-08 19:10:00	2020-04-10 16:15:00	111
2020-04-10 22:40:00	2020-04-13 17:20:00	112
2020-04-13 18:40:00	2020-04-15 01:10:00	113
2020-04-15 02:30:00	2020-04-18 17:55:00	114
2020-04-18 20:30:00	2020-04-20 02:00:00	115
2020-04-20 02:40:00	2020-04-20 15:05:00	116
2020-04-20 19:00:00	2020-04-21 22:55:00	117
2020-04-21 23:10:00	2020-04-24 15:45:00	118
2020-04-24 23:15:00	2020-04-25 15:10:00	119
2020-04-26 01:45:00	2020-04-26 15:15:00	120
2020-04-26 19:25:00	2020-04-27 15:10:00	121
2020-04-28 01:45:00	2020-04-28 15:15:00	122
2020-04-29 01:30:00	2020-04-29 15:10:00	123
2020-04-30 01:20:00	2020-04-30 15:10:00	124
2020-04-30 20:55:00	2020-05-01 15:20:00	125
2020-05-02 00:25:00	2020-05-02 15:40:00	126
2020-05-02 23:30:00	2020-05-03 16:00:00	127
2020-05-04 00:15:00	2020-05-04 15:10:00	128
2020-05-04 23:50:00	2020-05-05 14:40:00	129
2020-05-05 18:05:00	2020-05-05 20:05:00	130
2020-05-05 22:45:00	2020-05-06 14:45:00	131
2020-05-06 22:40:00	2020-05-07 15:20:00	132
2020-05-07 18:10:00	2020-05-08 17:00:00	133
2020-05-08 23:25:00	2020-05-09 15:50:00	134
2020-05-09 17:30:00	2020-05-13 15:05:00	135
2020-05-13 21:00:00	2020-05-14 14:30:00	136
2020-05-14 22:00:00	2020-05-15 14:45:00	137
2020-05-15 22:05:00	2020-05-16 14:45:00	138
2020-05-16 21:30:00	2020-05-17 13:40:00	139
2020-05-17 21:15:00	2020-05-18 13:20:00	140
2020-05-18 20:50:00	2020-05-19 13:50:00	141
2020-05-19 20:35:00	2020-05-20 17:20:00	142
2020-05-20 20:40:00	2020-05-21 15:25:00	143
2020-05-21 18:40:00	2020-05-26 15:15:00	144
2020-05-26 20:15:00	2020-05-27 14:35:00	145
2020-05-27 19:10:00	2020-05-28 12:25:00	146
2020-05-28 13:10:00	2020-05-29 16:25:00	147
2020-05-29 17:20:00	2020-05-30 13:05:00	148
2020-05-30 13:40:00	2020-05-31 13:55:00	149
2020-05-31 17:30:00	2020-06-01 12:55:00	150
2020-06-01 13:45:00	2020-08-09 17:55:00	151
2020-08-09 18:00:00	2020-08-17 12:55:00	152
2020-08-17 20:30:00	2020-08-18 13:10:00	153
2020-08-18 18:40:00	2020-08-19 13:25:00	154
2020-08-19 16:05:00	2020-08-19 18:25:00	155
2020-08-19 21:00:00	2020-08-20 15:30:00	156
2020-08-20 21:40:00	2020-08-21 13:55:00	157
2020-08-21 22:05:00	2020-08-22 14:05:00	158
2020-08-22 22:10:00	2020-08-23 13:05:00	159
2020-08-23 17:05:00	2020-08-23 21:05:00	160
2020-08-23 21:50:00	2020-08-24 14:55:00	161
2020-08-24 21:35:00	2020-08-25 13:20:00	162
2020-08-25 13:25:00	2020-08-26 15:55:00	163
2020-08-26 20:55:00	2020-08-27 14:05:00	164
2020-08-27 15:20:00	2020-08-27 16:55:00	165
2020-08-27 18:15:00	2020-08-28 18:05:00	166
2020-08-28 22:00:00	2020-08-29 18:35:00	167
2020-08-29 19:55:00	2020-08-30 23:10:00	168
2020-08-30 23:20:00	2020-09-01 13:40:00	169
2020-09-01 14:05:00	2020-09-03 15:25:00	170
2020-09-03 16:05:00	2020-09-03 17:45:00	171
2020-09-03 20:40:00	2020-09-04 13:45:00	172
2020-09-04 20:00:00	2020-09-05 14:40:00	173
2020-09-05 23:55:00	2020-09-06 13:50:00	174
2020-09-06 15:20:00	2020-09-06 18:05:00	175
2020-09-06 20:05:00	2020-09-07 13:45:00	176
2020-09-07 14:10:00	2020-09-11 13:40:00	177
2020-09-11 13:55:00	2020-09-12 13:40:00	178
2020-09-12 14:05:00	2020-09-13 13:40:00	179
2020-09-13 13:55:00	2020-09-15 13:35:00	180
2020-09-15 13:50:00	2020-09-16 19:10:00	181
2020-09-16 20:25:00	2020-09-17 18:45:00	182
2020-09-17 21:30:00	2020-09-18 14:10:00	183
2020-09-19 00:20:00	2020-09-19 14:45:00	184
2020-09-19 21:55:00	2020-09-20 15:15:00	185
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2020-09-27 19:10:00	2020-09-28 20:45:00	193